The global aim of this project is to increase our understanding of the diverse microbial community that inhabits the human gastrointestinal (GI) tract. This microbiota plays essential roles in human health, including a significant contribution to the digestive process, promotion of gut maturation and integrity and modulation of the immune system. Moreover, the microbiota interacts with pathogenic agents in several complex ways. On one hand, resident bacteria exert a protective barrier effect against enteropathogens; but, on the other, they could contribute to enrich the arsenal of incoming pathogens through horizontal transmission of genes involved in host-microbe interaction or antibiotic resistance. In addition, many normally benign GI commensals have the potential to become opportunistic pathogens in compromised hosts. Elucidating the composition and coding capabilities of the GI microbiota is therefore crucial for a comprehensive analysis of infectious disease. To advance towards this goal, we will produce large-insert bacterial artificial chromosome (BAC) libraries from genomic DNA isolated directly from fecal samples. The availability of BAC libraries will allow for a deep characterization of the GI microbiota by providing extensive genomic sequences that will serve to elucidate the coding capabilities as well as the phylogenetic positions of the members of this community. Given that the composition of the GI microbiota varies greatly with age and diet, we have chosen to generate BAC libraries from two very distinct stages of microbiota development: adults and breast-feeding infants, as represented by mother and child. Because of the widespread use of mice as an experimental system to study both infectious diseases in general and the GI microbiota in particular, we will also generate BAC libraries for mouse mother and suckling pup. To maximize our insight into the evolution and ecology of infectious disease, we will focus our sequencing efforts towards genomic regions relevant to pathogenicity and other ecological interactions, both among the microbial community members and between microbes and host.